﻿// Accord Datasets Library
// The Accord.NET Framework
// http://accord-framework.net
//
// Copyright © César Souza, 2009-2017
// cesarsouza at gmail.com
//
//    This library is free software; you can redistribute it and/or
//    modify it under the terms of the GNU Lesser General Public
//    License as published by the Free Software Foundation; either
//    version 2.1 of the License, or (at your option) any later version.
//
//    This library is distributed in the hope that it will be useful,
//    but WITHOUT ANY WARRANTY; without even the implied warranty of
//    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
//    Lesser General Public License for more details.
//
//    You should have received a copy of the GNU Lesser General Public
//    License along with this library; if not, write to the Free Software
//    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
//

namespace Accord.DataSets
{
    using Accord.DataSets.Base;
    using Accord.Math;
    using System;

    /// <summary>
    ///   University of Wisconsin's (Prognostic) Breast Cancer data set.
    /// </summary>
    /// 
    /// <remarks>
    /// <para>
    ///   Each record represents follow-up data for one breast cancer case. These are consecutive 
    ///   patients seen by Dr. Wolberg since 1984, and include only those cases exhibiting invasive
    ///   breast cancer and no evidence of distant metastases at the time of diagnosis. </para>
    /// <para>
    ///   The first 30 features are computed from a digitized image of a fine needle aspirate (FNA) 
    ///   of a breast mass.They describe characteristics of the cell nuclei present in the image. A
    ///   few of the images can be found at http://www.cs.wisc.edu/~street/images/ </para>
    /// <para>
    ///   The separation described above was obtained using Multisurface Method-Tree(MSM-T) [K.P.Bennett, 
    ///   "Decision Tree Construction Via Linear Programming." Proceedings of the 4th Midwest Artificial 
    ///   Intelligence and Cognitive Science Society, pp. 97-101, 1992], a classification method which uses
    ///   linear programming to construct a decision tree. Relevant features were selected using an exhaustive
    ///   search in the space of 1-4 features and 1-3 separating planes.</para>
    /// <para>
    ///   The actual linear program used to obtain the separating plane in the 3-dimensional space is that 
    ///   described in: [K.P.Bennett and O.L.Mangasarian: "Robust Linear Programming Discrimination of Two 
    ///   Linearly Inseparable Sets", Optimization Methods and Software 1, 1992, 23-34]. </para>
    /// <para>
    ///   The Recurrence Surface Approximation (RSA) method is a linear programming model which predicts Time
    ///   To Recur using both recurrent and nonrecurrent cases.See references (i) and (ii) above for details 
    ///   of the RSA method.</para>
    ///   
    /// <para>
    ///   References:
    ///   <list type="bullet">
    ///     <item><description><a href="https://archive.ics.uci.edu/ml/datasets/Breast+Cancer+Wisconsin+(Prognostic)">
    ///       Lichman, M. "UCI Machine Learning Repository - Breast Cancer Wisconsin (Prognostic) Data Set."
    ///       Irvine, CA: University of California, School of Information and Computer Science, 2013</a>
    ///       </description></item>
    ///    </list></para>
    /// </remarks>
    /// 
    public class WisconsinPrognosticBreastCancer
    {
        /// <summary>
        ///   Gets the data instance features contained in Wisconsin's Breast Cancer dataset.
        /// </summary>
        /// 
        public double[][] Features { get; private set; }

        /// <summary>
        ///   Gets identifiers for each of the instances contained in Wisconsin's Breast Cancer dataset.
        /// </summary>
        /// 
        public int[] InstanceIds { get; private set; }

        /// <summary>
        ///   Gets the outcome for each of the data instances in the dataset. The outcomes can be either
        ///   0 (Recurring) or 1 (Non-recurring) depending on what happened at the time instants stored 
        ///   in <see cref="Time"/>.
        /// </summary>
        /// 
        public int[] Outcome { get; private set; }

        /// <summary>
        ///   Gets the time until a possible <see cref="Outcome"/> has been detected. If the outcome has been
        ///   ruled as recurring (0), it means that the cancer reocurred after the given number of days after 
        ///   the initial treatment performed for this patient. If the outcome is marker as non-recurring (1), 
        ///   it means the cancer has not been observed until the given number of days marked in this array.
        /// </summary>
        /// 
        public int[] Time { get; private set; }

        /// <summary>
        ///   Gets the class labels associated with each <see cref="Features">instance</see>
        ///   in Wisconsin's Breast Cancer dataset.
        /// </summary>
        /// 
        public int[] ClassLabels { get; private set; }

        /// <summary>
        ///   Gets the outcome labels in Wiscosin's Prognostic Breast Cancer dataset:
        ///   "Recurring" (cancer has re-orcurred during observation period), "Nonrecurring" (disease-free during observation period).
        /// </summary>
        /// 
        public string[] ClassNames { get; private set; }

        /// <summary>
        ///   Gets the variable names in Wisconsin's Breast Cancer dataset: 
        ///  "radius" (mean of distances from center to points on the perimeter),
        ///  "texture" (standard deviation of gray-scale values),
        ///  "perimeter",
        ///  "area",
        ///  "smoothness" (local variation in radius lengths),
        ///  "compactness" (perimeter^2 / area - 1.0),
        ///  "concavity" (severity of concave portions of the contour),
        ///  "concave points" (number of concave portions of the contour),
        ///  "symmetry",
        ///  "fractal dimension" ("coastline approximation" - 1)
        /// </summary>
        /// 
        public string[] VariableNames { get; private set; }

        /// <summary>
        ///   Prepares the Wisconsin's (Diagnostic) Breast Cancer dataset.
        /// </summary>
        /// 
        public WisconsinPrognosticBreastCancer()
        {
            object[,] data =
            {
                {119513,"N",31,18.02,27.6,117.5,1013,0.09489,0.1036,0.1086,0.07055,0.1865,0.06333,0.6249,1.89,3.972,71.55,0.004433,0.01421,0.03233,0.009854,0.01694,0.003495,21.63,37.08,139.7,1436,0.1195,0.1926,0.314,0.117,0.2677,0.08113,5,5                  },
                {8423,"N",61,17.99,10.38,122.8,1001,0.1184,0.2776,0.3001,0.1471,0.2419,0.07871,1.095,0.9053,8.589,153.4,0.006399,0.04904,0.05373,0.01587,0.03003,0.006193,25.38,17.33,184.6,2019,0.1622,0.6656,0.7119,0.2654,0.4601,0.1189,3,2                    },
                {842517,"N",116,21.37,17.44,137.5,1373,0.08836,0.1189,0.1255,0.0818,0.2333,0.0601,0.5854,0.6105,3.928,82.15,0.006167,0.03449,0.033,0.01805,0.03094,0.005039,24.9,20.98,159.1,1949,0.1188,0.3449,0.3414,0.2032,0.4334,0.09067,2.5,0                },
                {843483,"N",123,11.42,20.38,77.58,386.1,0.1425,0.2839,0.2414,0.1052,0.2597,0.09744,0.4956,1.156,3.445,27.23,0.00911,0.07458,0.05661,0.01867,0.05963,0.009208,14.91,26.5,98.87,567.7,0.2098,0.8663,0.6869,0.2575,0.6638,0.173,2,0                  },
                {843584,"R",27,20.29,14.34,135.1,1297,0.1003,0.1328,0.198,0.1043,0.1809,0.05883,0.7572,0.7813,5.438,94.44,0.01149,0.02461,0.05688,0.01885,0.01756,0.005115,22.54,16.67,152.2,1575,0.1374,0.205,0.4,0.1625,0.2364,0.07678,3.5,0                    },
                {843786,"R",77,12.75,15.29,84.6,502.7,0.1189,0.1569,0.1664,0.07666,0.1995,0.07164,0.3877,0.7402,2.999,30.85,0.007775,0.02987,0.04561,0.01357,0.01774,0.005114,15.51,20.37,107.3,733.2,0.1706,0.4196,0.5999,0.1709,0.3485,0.1179,2.5,0             },
                {844359,"N",60,18.98,19.61,124.4,1112,0.09087,0.1237,0.1213,0.0891,0.1727,0.05767,0.5285,0.8434,3.592,61.21,0.003703,0.02354,0.02222,0.01332,0.01378,0.003926,23.39,25.45,152.6,1593,0.1144,0.3371,0.299,0.1922,0.2726,0.09581,1.5,null              },
                {844582,"R",77,13.71,20.83,90.2,577.9,0.1189,0.1645,0.09366,0.05985,0.2196,0.07451,0.5835,1.377,3.856,50.96,0.008805,0.03029,0.02488,0.01448,0.01486,0.005412,17.06,28.14,110.6,897,0.1654,0.3682,0.2678,0.1556,0.3196,0.1151,4,10                },
                {844981,"N",119,13,21.82,87.5,519.8,0.1273,0.1932,0.1859,0.09353,0.235,0.07389,0.3063,1.002,2.406,24.32,0.005731,0.03502,0.03553,0.01226,0.02143,0.003749,15.49,30.73,106.2,739.3,0.1703,0.5401,0.539,0.206,0.4378,0.1072,2,1                     },
                {845010,"N",76,12.46,24.04,83.97,475.9,0.1186,0.2396,0.2273,0.08543,0.203,0.08243,0.2976,1.599,2.039,23.94,0.007149,0.07217,0.07743,0.01432,0.01789,0.01008,15.09,40.68,97.65,711.4,0.1853,1.058,1.105,0.221,0.4366,0.2075,6,20                   },
                {845636,"N",123,16.02,23.24,102.7,797.8,0.08206,0.06669,0.03299,0.03323,0.1528,0.05697,0.3795,1.187,2.466,40.51,0.004029,0.009269,0.01101,0.007591,0.0146,0.003042,19.19,33.88,123.8,1150,0.1181,0.1551,0.1459,0.09975,0.2948,0.08452,2,0         },
                {846100,"N",125,15.78,17.89,103.6,781,0.0971,0.1292,0.09954,0.06606,0.1842,0.06082,0.5058,0.9849,3.564,54.16,0.005771,0.04061,0.02791,0.01282,0.02008,0.004144,20.42,27.28,136.5,1299,0.1396,0.5609,0.3965,0.181,0.3792,0.1048,1.4,0              },
                {846381,"N",117,15.85,23.95,103.7,782.7,0.08401,0.1002,0.09938,0.05364,0.1847,0.05338,0.4033,1.078,2.903,36.58,0.009769,0.03126,0.05051,0.01992,0.02981,0.003002,16.84,27.66,112,876.5,0.1131,0.1924,0.2322,0.1119,0.2809,0.06287,1,0             },
                {847990,"R",36,14.54,27.54,96.73,658.8,0.1139,0.1595,0.1639,0.07364,0.2303,0.07077,0.37,1.033,2.879,32.55,0.005607,0.0424,0.04741,0.0109,0.01857,0.005466,17.46,37.13,124.1,943.2,0.1678,0.6577,0.7026,0.1712,0.4218,0.1341,6,6                   },
                {848406,"N",123,14.68,20.13,94.74,684.5,0.09867,0.072,0.07395,0.05259,0.1586,0.05922,0.4727,1.24,3.195,45.4,0.005718,0.01162,0.01998,0.01109,0.0141,0.002085,19.07,30.88,123.4,1138,0.1464,0.1871,0.2914,0.1609,0.3029,0.08216,1.1,0              },
                {848620,"R",10,16.13,20.68,108.1,798.8,0.117,0.2022,0.1722,0.1028,0.2164,0.07356,0.5692,1.073,3.854,54.18,0.007026,0.02501,0.03188,0.01297,0.01689,0.004142,20.96,31.48,136.8,1315,0.1789,0.4233,0.4784,0.2073,0.3706,0.1142,3,1                  },
                {8511133,"N",20,15.34,14.26,102.5,704.4,0.1073,0.2135,0.2077,0.09756,0.2521,0.07032,0.4388,0.7096,3.384,44.91,0.006789,0.05328,0.06446,0.02252,0.03672,0.004394,18.07,19.08,125.1,980.9,0.139,0.5954,0.6305,0.2393,0.4667,0.09946,1.3,0           },
                {851509,"R",10,21.16,23.04,137.2,1404,0.09428,0.1022,0.1097,0.08632,0.1769,0.05278,0.6917,1.127,4.303,93.99,0.004728,0.01259,0.01715,0.01038,0.01083,0.001987,29.17,35.59,188,2615,0.1401,0.26,0.3155,0.2009,0.2822,0.07526,4,1                   },
                {852552,"N",96,16.65,21.38,110,904.6,0.1121,0.1457,0.1525,0.0917,0.1995,0.0633,0.8068,0.9017,5.455,102.6,0.006048,0.01882,0.02741,0.0113,0.01468,0.002801,26.46,31.56,177,2215,0.1805,0.3578,0.4695,0.2095,0.3613,0.09564,3,0                     },
                {852631,"N",116,17.14,16.4,116,912.7,0.1186,0.2276,0.2229,0.1401,0.304,0.07413,1.046,0.976,7.276,111.4,0.008029,0.03799,0.03732,0.02397,0.02308,0.007444,22.25,21.4,152.4,1461,0.1545,0.3949,0.3853,0.255,0.4066,0.1059,4.4,1                     },
                {852763,"N",103,14.58,21.53,97.41,644.8,0.1054,0.1868,0.1425,0.08783,0.2252,0.06924,0.2545,0.9832,2.11,21.05,0.004452,0.03055,0.02681,0.01352,0.01454,0.003711,17.62,33.21,122.4,896.9,0.1525,0.6643,0.5539,0.2701,0.4264,0.1275,2.5,0            },
                {852781,"N",16,18.61,20.25,122.1,1094,0.0944,0.1066,0.149,0.07731,0.1697,0.05699,0.8529,1.849,5.632,93.54,0.01075,0.02722,0.05081,0.01911,0.02293,0.004217,21.31,27.26,139.9,1403,0.1338,0.2117,0.3446,0.149,0.2341,0.07421,3.4,13                },
                {852973,"N",52,15.3,25.27,102.4,732.4,0.1082,0.1697,0.1683,0.08751,0.1926,0.0654,0.439,1.012,3.498,43.5,0.005233,0.03057,0.03576,0.01083,0.01768,0.002967,20.27,36.71,149.3,1269,0.1641,0.611,0.6335,0.2024,0.4027,0.09876,2,0                    },
                {853201,"N",94,17.57,15.05,115,955.1,0.09847,0.1157,0.09875,0.07953,0.1739,0.06149,0.6003,0.8225,4.655,61.1,0.005627,0.03033,0.03407,0.01354,0.01925,0.003742,20.01,19.52,134.9,1227,0.1255,0.2812,0.2489,0.1456,0.2756,0.07919,4,0               },
                {853612,"N",116,11.84,18.7,77.93,440.6,0.1109,0.1516,0.1218,0.05182,0.2301,0.07799,0.4825,1.03,3.475,41,0.005551,0.03414,0.04205,0.01044,0.02273,0.005667,16.82,28.12,119.4,888.7,0.1637,0.5775,0.6956,0.1546,0.4761,0.1402,3,2                   },
                {853826,"N",87,17.02,23.98,112.8,899.3,0.1197,0.1496,0.2417,0.1203,0.2248,0.06382,0.6009,1.398,3.999,67.78,0.008268,0.03082,0.05042,0.01112,0.02102,0.003854,20.88,32.09,136.1,1344,0.1634,0.3559,0.5588,0.1847,0.353,0.08482,1.3,1               },
                {854002,"N",53,19.27,26.47,127.9,1162,0.09401,0.1719,0.1657,0.07593,0.1853,0.06261,0.5558,0.6062,3.528,68.17,0.005015,0.03318,0.03497,0.009643,0.01543,0.003896,24.15,30.9,161.4,1813,0.1509,0.659,0.6091,0.1785,0.3672,0.1123,3.5,0              },
                {854039,"N",109,16.13,17.88,107,807.2,0.104,0.1559,0.1354,0.07752,0.1998,0.06515,0.334,0.6857,2.183,35.03,0.004185,0.02868,0.02664,0.009067,0.01703,0.003817,20.21,27.26,132.7,1261,0.1446,0.5804,0.5274,0.1864,0.427,0.1233,2.5,0                },
                {854253,"N",12,16.74,21.59,110.1,869.5,0.0961,0.1336,0.1348,0.06018,0.1896,0.05656,0.4615,0.9197,3.008,45.19,0.005776,0.02499,0.03695,0.01195,0.02789,0.002665,20.01,29.02,133.5,1229,0.1563,0.3835,0.5409,0.1813,0.4863,0.08633,1.5,null            },
                {854268,"N",31,14.25,21.72,93.63,633,0.09823,0.1098,0.1319,0.05598,0.1885,0.06125,0.286,1.019,2.657,24.91,0.005878,0.02995,0.04815,0.01161,0.02028,0.004022,15.89,30.36,116.2,799.6,0.1446,0.4238,0.5186,0.1447,0.3591,0.1014,3,13                },
                {855133,"N",72,14.99,25.2,95.54,698.8,0.09387,0.05131,0.02398,0.02899,0.1565,0.05504,1.214,2.188,8.077,106,0.006883,0.01094,0.01818,0.01917,0.007882,0.001754,14.99,25.2,95.54,698.8,0.09387,0.05131,0.02398,0.02899,0.1565,0.05504,3.5,10        },
                {855138,"N",76,13.48,20.82,88.4,559.2,0.1016,0.1255,0.1063,0.05439,0.172,0.06419,0.213,0.5914,1.545,18.52,0.005367,0.02239,0.03049,0.01262,0.01377,0.003187,15.53,26.02,107.3,740.4,0.161,0.4225,0.503,0.2258,0.2807,0.1071,2.5,0                 },
                {855167,"N",34,13.44,21.58,86.18,563,0.08162,0.06031,0.0311,0.02031,0.1784,0.05587,0.2385,0.8265,1.572,20.53,0.00328,0.01102,0.0139,0.006881,0.0138,0.001286,15.93,30.25,102.5,787.9,0.1094,0.2043,0.2085,0.1112,0.2994,0.07146,1.5,0             },
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                {855625,"R",9,19.07,24.81,128.3,1104,0.09081,0.219,0.2107,0.09961,0.231,0.06343,0.9811,1.666,8.83,104.9,0.006548,0.1006,0.09723,0.02638,0.05333,0.007646,24.09,33.17,177.4,1651,0.1247,0.7444,0.7242,0.2493,0.467,0.1038,2.3,0                    },
                {856106,"N",114,13.28,20.28,87.32,545.2,0.1041,0.1436,0.09847,0.06158,0.1974,0.06782,0.3704,0.8249,2.427,31.33,0.005072,0.02147,0.02185,0.00956,0.01719,0.003317,17.38,28,113.1,907.2,0.153,0.3724,0.3664,0.1492,0.3739,0.1027,2.6,1              },
                {856385,"N",76,13.17,21.81,85.42,531.5,0.09714,0.1047,0.08259,0.05252,0.1746,0.06177,0.1938,0.6123,1.334,14.49,0.00335,0.01384,0.01452,0.006853,0.01113,0.00172,16.23,29.89,105.5,740.7,0.1503,0.3904,0.3728,0.1607,0.3693,0.09618,1.7,1          },
                {857010,"R",8,18.65,17.6,123.7,1076,0.1099,0.1686,0.1974,0.1009,0.1907,0.06049,0.6289,0.6633,4.293,71.56,0.006294,0.03994,0.05554,0.01695,0.02428,0.003535,22.82,21.32,150.6,1567,0.1679,0.509,0.7345,0.2378,0.3799,0.09185,1.8,0                 },
                {85715,"N",111,13.17,18.66,85.98,534.6,0.1158,0.1231,0.1226,0.0734,0.2128,0.06777,0.2871,0.8937,1.897,24.25,0.006532,0.02336,0.02905,0.01215,0.01743,0.003643,15.67,27.95,102.8,759.4,0.1786,0.4166,0.5006,0.2088,0.39,0.1179,1,1                 },
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                {9411286,"N",3,19.22,27.18,128.8,1134,0.109,0.1777,0.2138,0.1116,0.1924,0.06389,0.497,2.403,4.493,61.18,0.006133,0.04109,0.05917,0.01756,0.0218,0.004305,22.57,44.6,161,1565,0.1501,0.513,0.6841,0.2099,0.3484,0.09774,0.8,1                      },
                {9411300,"N",3,14.72,25.26,99.28,657.5,0.1174,0.2112,0.1729,0.09465,0.2079,0.07496,0.3405,1.158,2.188,26.12,0.004957,0.04553,0.05166,0.01597,0.02539,0.005548,16.67,31.97,111.6,814.8,0.1464,0.5352,0.5655,0.1974,0.3778,0.1132,1.7,21            },
                {942640,"N",10,22.52,21.92,146.9,1597,0.07592,0.09162,0.06862,0.06367,0.1728,0.05262,1.374,2.312,9.938,192.4,0.004422,0.02679,0.02433,0.02036,0.02486,0.003922,24.67,24.81,162.1,1902,0.08191,0.1319,0.1056,0.09378,0.2061,0.05788,6,2            },
                {943471,"N",8,15.44,31.18,101,740.4,0.09399,0.1062,0.1375,0.065,0.1735,0.06105,0.3235,1.839,1.971,32.61,0.006178,0.02088,0.02834,0.01079,0.02122,0.003168,17.34,41.48,112.6,929,0.1272,0.2362,0.2975,0.1286,0.2914,0.08024,1.5,0                  },
                {94547,"N",12,17.17,29.19,110,915.3,0.08952,0.06655,0.06583,0.05068,0.1793,0.05392,0.6101,1.425,3.827,63.02,0.00689,0.01556,0.03155,0.009714,0.02734,0.001377,20.76,36.66,132.5,1295,0.1261,0.1572,0.2141,0.0952,0.3362,0.06033,3.7,0             },
                {947204,"R",3,21.42,22.84,145,1440,0.107,0.1939,0.238,0.1318,0.1884,0.06472,1.085,0.8469,8.308,142.5,0.006831,0.03541,0.04948,0.0177,0.01481,0.003979,28.34,27.98,198.3,2375,0.1498,0.4379,0.5411,0.2215,0.2832,0.08981,3,null                       },
                {947489,"N",6,16.7,28.13,110.3,885.4,0.08896,0.1131,0.1012,0.04989,0.189,0.06035,0.6052,1.235,4.243,63.91,0.007767,0.02631,0.03957,0.01411,0.01957,0.003606,19.74,34.92,128.8,1213,0.133,0.2808,0.3455,0.1317,0.3035,0.08036,3.5,0                },
            };

            ClassNames = new[]
            {
                "Recurring", "Nonrecurring"
            };

            VariableNames = new[]
            {
                "ID number",
                "radius",            // (mean of distances from center to points on the perimeter)
                "texture",           // (standard deviation of gray - scale values)
                "perimeter",         // 
                "area",              // 
                "smoothness",        // (local variation in radius lengths)
                "compactness",       // (perimeter ^ 2 / area - 1.0)
                "concavity",         // (severity of concave portions of the contour)
                "concave points",    // (number of concave portions of the contour)
                "symmetry",          // 
                "fractal dimension", // ("coastline approximation" - 1)
            };


            int n = data.GetLength(0);
            Features = new double[n][];
            InstanceIds = new int[n];
            ClassLabels = new int[n];
            for (int i = 0; i < Features.Length; i++)
            {
                Features[i] = new double[10];
                for (int j = 0; j < Features[i].Length; j++)
                    Features[i][j] = (double)data[i, j + 3];
                ClassLabels[i] = (string)data[i, 1] == "R" ? 0 : 1;
                InstanceIds[i] = (int)data[i, 0];
                Time[i] = (int)data[i, 2];
            }

        }

    }
}
